Download GATK version 1.4

ethering

Hi, I want to run GATK in Galaxy and the required version is 1.4. Can you tell me where I can download this from? I've got the source for version 1.4 from github, so I can build it if need be, but I was wondering if there's a repository for older binaries. Many thanks, Graham

Geraldine_VdAuwera

Hi Graham, No, we don't provide older binaries, you'll need to compile your own. Note that we strongly recommend using more recent versions, as older versions have bugs that have been fixed in the newer... Good luck!

Geraldine_VdAuwera

Oops, correction -- we do have the old binaries, they're on our public FTP server.

Geraldine_VdAuwera

And another correction -- they're in a private dir on the ftp, so I've copied the most relevant ones to our public dropbox here: https://www.dropbox.com/sh/1misjysdehceq4h/GnQB948vMl

jorges1000

I tried version 1.6-13-g91f02df in Galaxy and it works fine, at least for the tools I have tested.

Tgong

Can I get the GATK version 2.0 but before 2.4? I want to use the somaticindeldetector. Thanks!

Geraldine_VdAuwera

Hi @Tgong,

We're not hosting the binaries, but if you want you can download the source code and build whichever version you want. See the Downloads page for access to the code repository.

arkal

so i have NO idea t all how to get the binary for gatk 2.3.9 from the source code....sigh the inconvenience of not being familiar with java... anyway.... can anyone help me out here and post the binary for 2.3.9? i need t use somatic indel detector

Geraldine_VdAuwera

Hi @arkal,

It's actually really easy to build from source, you should give it a try -- you will feel empowered for future work!

1. Get the package for the version you want from this page: https://github.com/broadgsa/gatk-protected/tags

2. From your terminal/console, navigate to the directory containing the source code. There, you run the command:

   ant clean dist

This will do everything for you. The compiled binary will be in the newly-created dist directory.